Passion in the Desert A movie review by "Average Joe" Barlow (c) Copyright 1998
STARRING: Ben Daniels, Michel Piccoli DIRECTOR: Lavina Currier WRITERS: Lavina Currier and Martin Edmunds RATED/YEAR: PG-13/1998
This is a strange one, kids. Even though independent films frequently tackle subjects which Hollywood considers taboo or unmarketable, "Passion in the Desert" raises the bar to new heights. Interracial love stories are uncommon enough on the silver screen... but interspecies? Such is Lavina Currier's vision. The tale, adapted from a short story by Honore' de Balzac, opens in the Egyptian desert circa 1798 A.D. A small group of soldiers have been assigned to escort Napolean's favorite artist (played by Michel Piccoli) on a cross-country march as he draws and paints pictures of the landscape. The land is staggeringly hostile, and the group has its hands full coping with the crippling heat, scorpions, sandstorms, and frequent attacks by rogue nomads. During a particularly fierce sandstorm, the artist and a solider named Augustin Robert (Ben Daniels) get separated from the rest of their group. They find themselves lost, hundreds of miles from civilization, with no supplies to speak of. They realise the severity of their predicament at once ("The desert is totally unpredictable, like living in the tempest of a woman's heart," observes the artist in one of the film's most memorable lines) and immediately begin the search for the rest of their group. The heat claims their horses fairly quickly, and the two men manage to survive only by drinking the artist's paint. Even so, the elderly artist is quickly overcome by the sweltering temperatures, and Augustin (who is the spitting image of Kenneth Branagh) is forced to leave his friend beneath a small tree, promising to return with help as soon as he can. Little more than a zombie at this point, Augustin chances upon a nomad camp which appears to be deserted. In a wonderfully tense scene, he sneaks inside, searching for food and water. I won't reveal what he discovers there (it's one of the film's best scenes), but soon after, our hero finds himself trapped in a cave with a leopard who won't allow him to leave. No matter how he attempts to flee, the leopard always outsmarts him. Augustin realises that he must earn the creature's respect, and thus begins a fascinating game of wits. It's "The English Patient" meets "Dr. Dolittle." Yes, he succeeds, and the two become friends. It's at this point that the film switches gears, changing from an exciting drama into something else completely. Augustin and the leopard become very close indeed as they learn to trust and respect each other. They share food and water. They cuddle and play. They hunt together. They kiss. They lick each other's skin. God help us, they even slow dance. In short, they... they... fall in love, basically. No, I'm not making this up. Now it's "Dr. Dolittle" meets "Lolita." From this point on, I had no idea who I was supposed to root for. Do we hope Augustin makes it back to civilization safely? That he and the leopard live happily ever after? That the SPCA shows up and shoots them both? I'm not sure, and that may be the film's biggest flaw: we have no idea what the ultimate goal of the movie is, nor why Augustin forsakes the artist after he befriends the leopard. Surely he could've brought some water to the old man. But no... from the moment he enters the nomad camp, he never seems to think about his companion again. Why? I have no idea. However, you will not see a single movie this year that's better photographed than "Passion." One could literally take a random freeze- frame from any moment of the film and have a "National Geographic" cover photo. From the innovative use of camera angles and shadows, down to the color of the costumes and the sky itself, this is a movie whose images have been meticulously planned, down to the smallest detail. Visually, it makes "Titanic" look like a home movie (and considering I saw "Titanic" five times because of its visuals, that should tell you something). Particularly impressive is the scene in which we see the leopard for the first time: darkness. Then, a pair of glowing green eyes pierce the gloom. Gradually, the leopard comes into view... but it looks as though the director is not so much lighting the set as removing the darkness. Finally, we get our first look at the entire creature. We won't soon forget it. The music is also wonderful. Composed by Jose' Nieto (whose name I'd never heard before), it features some lovely orchestral work highlighted by Egyptian instruments. Best of all, Celine Dion is noticeably absent. I'll be buying this soundtrack. The climax of the film is disturbing, but not unexpected. Still, it appears with a suddenness that's a little disorienting. The movie just ends, as though the production suddenly realised they didn't have enough money to buy more film and had to wrap everything up quickly. The performance of Ben Daniels in the role of Augustin is admirable. He conveys all the emotions we'd expect his character to be feeling, and never seems to be uncomfortable with the material. We always believe his sincerity, even as we question his sanity. (Yes, that's a complement.) I'd like to see more of his work in the future. Truth be told, I found the audience's response just as interesting as the film itself. Startled gasps and muffled giggles floated around the surprisingly crowded theater for much of the screening. The woman sitting in front of me stormed out after only an hour and didn't return, but a lady sitting towards the back wept loudly during the end credits. And as the audience filed out, I noticed at least a dozen people wearing expressions similar to my own-- expressions that said, quite simply, "Did I really see that? Is this a joke?" This comparison will probably raise a few eyebrows, but "Passion in the Desert" reminded me of "Dances with Wolves" in many ways. Both films are set in the past, and follow the story of a military officer separated from the rest of his group. Both characters befriend an animal, are forever changed by what happens to them, and are reluctant to return to their former way of life when the time comes. In all honesty, I think I liked "Passion" better. This film isn't a must-see, but it's not the worst film out there, either. The potentially disturbing story is countered by excellent acting, music, and cinematography. But be warned: there's quite a lot of violence, blood, and some full-frontal male nudity. Leave the kids at home.
RATING: 3.0 stars (out of a possible five)
This review was written: July 19, 1998 Copyright (c) 1998 by Joe Barlow. This review may be freely distributed as long as ABSOLUTELY NO CHANGES are made and this disclaimer remains attached. It may not be reproduced for profit without the written consent of the author. If you have comments or questions, please send them to: jbarlow at earthling dot net (substituting the appropriate symbols, to discourage spam).
----- "Average Joe" Barlow * MiSTie #73097 * Writer/musician/aspiring filmmaker<EMAIL_ADDRESS>http://www.ipass.net/~jbarlow {Remove YOUR PANTS to e-mail me.}
"More Reba! More Garth! And... Wynona!" -TV's Frank, Mystery Science Theater 3OOO
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Classes in Ruby
I'm not talking about DBC Classes! January 24th, 2015
Classes are quickly becoming my main focus point within Phase 0. A Class is simply like a foundation to create an object.   Each counterfeit bill, whether it be a single dollar bill, a five dollar bill, a ten, or a twenty are your objects of the templates. The template, which is your class, will create all your bills, even if they don't look all the same at the end result.
end
end
end
new_bill = Counterfeit.new(5)
new_bill.printing
What this is doing here is creating the class of "Counterfeit", initializing the "bills" to an instance variable of "bills". This allows the variable of bills to be used solely within the Class. Defining the method of printing will allow for us to later run the code that follows the "if". This next block of code will only print out the result of "Made a $x bill" where x is equal to the values seen in the code. So at the bottom of it, new_bill is the new object we are creating. The new_bill is going to be made new with the paramater of 5 (which is going to be a $5 bill). new_bill.printing is going to run the object through our new method "printing" and the result is going to be that the console will print out "Made a $5 bill". Cool huh?


{% extends "base.html" %} {% block title %}
Medieval catalogues > NEW FRIARS > Guildford-Dominican > Leland, c. 1536-40
{% endif %}7 identified entries found.
All data was derived from the List of Identifications by Professor Richard Sharpe.
{% if not printing %}
A key to codes used in the List is available (opens in new tab).{% endif %}


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module Observable
The Observer pattern (also known as publish/subscribe) provides a simple mechanism for one object to inform a set of interested third-party objects when its state changes.
Mechanism¶ ↑
The notifying class mixes in the Observable
module, which
provides the methods for managing the associated observer objects.
The observable object must:
-
assert that it has
#changed
-
call
#notify_observers
An observer subscribes to updates using #add_observer, which also specifies the method called via notify_observers. The default method for notify_observers is update.
Example¶ ↑
The following example demonstrates this nicely. A Ticker
,
when run, continually receives the stock Price
for its
@symbol
. A Warner
is a general observer of the
price, and two warners are demonstrated, a WarnLow
and a
WarnHigh
, which print a warning if the price is below or above
their set limits, respectively.
The update
callback allows the warners to run without being
explicitly called. The system is set up with the Ticker
and
several observers, and the observers do their duty without the top-level
code having to interfere.
Note that the contract between publisher and subscriber (observable and
observer) is not declared or enforced. The Ticker
publishes a
time and a price, and the warners receive that. But if you don't
ensure that your contracts are correct, nothing else can warn you.
require "observer" class Ticker ### Periodically fetch a stock price. include Observable def initialize(symbol) @symbol = symbol end def run last_price = nil loop do price = Price.fetch(@symbol) print "Current price: #{price}\n" if price != last_price changed # notify observers last_price = price notify_observers(Time.now, price) end sleep 1 end end end class Price ### A mock class to fetch a stock price (60 - 140). def self.fetch(symbol) 60 + rand(80) end end class Warner ### An abstract observer of Ticker objects. def initialize(ticker, limit) @limit = limit ticker.add_observer(self) end end class WarnLow < Warner def update(time, price) # callback for observer if price < @limit print "--- #{time.to_s}: Price below #@limit: #{price}\n" end end end class WarnHigh < Warner def update(time, price) # callback for observer if price > @limit print "+++ #{time.to_s}: Price above #@limit: #{price}\n" end end end ticker = Ticker.new("MSFT") WarnLow.new(ticker, 80) WarnHigh.new(ticker, 120) ticker.run
Produces:
Current price: 83 Current price: 75 --- Sun Jun 09 00:10:25 CDT 2002: Price below 80: 75 Current price: 90 Current price: 134 +++ Sun Jun 09 00:10:25 CDT 2002: Price above 120: 134 Current price: 134 Current price: 112 Current price: 79 --- Sun Jun 09 00:10:25 CDT 2002: Price below 80: 79
Public Instance Methods
Add observer
as an observer on this object. so that it will
receive notifications.
observer
-
the object that will be notified of changes.
func
-
Symbol naming the method that will be called when this Observable has changes.
This method must return true for
observer.respond_to?
and will receive*arg
when notify_observers is called, where*arg
is the value passed to notify_observers by this Observable
# File lib/observer.rb, line 127 def add_observer(observer, func=:update) @observer_peers = {} unless defined? @observer_peers unless observer.respond_to? func raise NoMethodError, "observer does not respond to `#{func}'" end @observer_peers[observer] = func end
Set the changed state of this object. Notifications
will be sent only if the changed state
is true
.
state
-
Boolean indicating the changed state of this Observable.
# File lib/observer.rb, line 168 def changed(state=true) @observer_state = state end
Returns true if this object's state has been changed since the last notify_observers call.
# File lib/observer.rb, line 176 def changed? if defined? @observer_state and @observer_state true else false end end
Return the number of observers associated with this object.
# File lib/observer.rb, line 154 def count_observers if defined? @observer_peers @observer_peers.size else 0 end end
Remove observer
as an observer on this object so that it will
no longer receive notifications.
observer
-
An observer of this Observable
# File lib/observer.rb, line 140 def delete_observer(observer) @observer_peers.delete observer if defined? @observer_peers end
Remove all observers associated with this object.
# File lib/observer.rb, line 147 def delete_observers @observer_peers.clear if defined? @observer_peers end
Notify observers of a change in state if this object's
changed state is true
.
This will invoke the method named in add_observer, passing
*arg
. The changed state is then set to false
.
*arg
-
Any arguments to pass to the observers.
# File lib/observer.rb, line 192 def notify_observers(*arg) if defined? @observer_state and @observer_state if defined? @observer_peers @observer_peers.each do |k, v| k.send v, *arg end end @observer_state = false end end


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President Buhari Congratulates Former President Jonathan On His 62nd Birthday
by Seyi AdebowalePresident Muhammadu Buhari has felicitated with former President Goodluck Jonathan on his 62nd birthday, by joining the nation in praying for longer life, good health and more strength to keep serving the nation.
President Buhari said this in a press release by the Special Adviser to the President on Media and Publicity Femi Adesina noting that he rejoices with family, friends and political associates of the former president, lauding him for good counsels to leaders within and outside Nigeria since he left office, sharing his experience of serving at different levels of governance.
President Buhari believes the former President’s legacy of humility and patriotism will continue to resonate, inspiring generations to come on the sacrifices made for the stability of democracy and promotion of sustainable development
The President then wishes the former President and his family more years of joyful celebrations.


Here are some of my favorite quotes from A Tale of Two Cities by Charles Dickens:
“I should like to ask you: -Does your childhood seem far off? Do the days when you sat at your mother’s knee, seem days of very long ago?
 For, as I draw closer and closer to the end, I travel in the circle, nearer and nearer to the beginning. It seems to be one of the kind smoothings and preparings of the way. My heart is touched now, by many remembrances that had long fallen asleep, of my pretty young mother (and I so old!), and by many associations of the days when what we call the World was not so real with me, and my faults were not confirmed in me."
“The wretched wife of the innocent man thus doomed to die, fell under the sentence, as if she had been mortally stricken. But, she uttered no sound; and so strong was the voice within her, representing that it was she of all the world who must uphold him in his misery and not augment it, that it quickly raised her, even from that shock.”


 For example, suppose you have a project that has several subprojects, then each subproject is a board and the full multiboard represents the project.
{% if archived %} View active multiboards {% else %} View archived multiboards {% endif %} {% if member and not archived %} New multiboard {% endif %}
{% if multiboards|length == 0 %} {% if archived %} There are no archived multiboards for this member. {% else %} There are no multiboards for this member. {% endif %} {% else %}| # | Name | Boards | Members | Actions |
| {{multiboard.id}} | {{multiboard.name}} | {% with num_multiboards=multiboard.boards.all.count %} {% if num_multiboards > 0 %} {% for board in multiboard.boards.all %} {{board.name}} {% endfor %} {% endif %} {% endwith %} | {% for member_i in multiboard.members.all %} {% endfor %} | Task board {% if member and member.id == multiboard.creator_id %} {% endif %} |


|
AJAXWarrior Help
|
| |
| Arrow keys |
Move your player |
| A |
Toggle between Talk and Attack mode (Blue border for Talk mode, Red for Attack mode)
|
| C |
Cast spell
|
| E |
Enter community (Must be standing on it)
|
| H |
This help window
|
| I |
Display inventory
|
| P |
Pick up item (Must be standing on it)
|
| S |
Save game
|
| W |
Switch weapon
|
-- Press SPACEBAR to return to game --
|


Welcome to the website of the Michigan Mathematical Association of Two-Year Colleges! MichMATYC is an affiliate of the
American Mathematical Association of Two Year Colleges (AMATYC) –
the national organization devoted soley to issues facing mathematics educators in the first two years of college.
Since its beginnings in 1981, a major focus of MichMATYC's mission has been professional development, which includes our
annual conference in October each year. Here you can learn about our history, become a member, explore member resources,
read our newsletter, visit links to professional organizations, and much more!


--- layout: post title: "The Week in Robots" date: 2015-09-12 08:35:00 +0000 tags: image: https://s3.amazonaws.com/audreywatters/known_copy_fragments.jpg imagecredits: https://www.flickr.com/photos/cogdog/15223631110/ ---
This post first appeared on aud.life
British man builds helicopter from 54 drones & garden chair
Jerry Brown Shoots Down Drone Privacy Bill
Silicon Valley is raiding tech academia: “Uber would like to buy your Robotics Department”
Your liberty will not survive combat drones
AI Software Goes Up Against Fourth Graders on Science Tests
Inept copyright bot sends 2600 a legal threat over ink blotches
How Ashley Madison Hid Its Fembot Con From Users and Investigators
The Future of the Automated Restaurant
The Automat Revival is Cool But Where’s the Robot Who Takes Off My Top Hat?


SmoothMethod¶
-
class
lgblearn.core.algorithms.algorithms.
SmoothMethod
¶ Bases:
object
Methods Summary
EMSmooth
(x, y[, theta, threshold, int_method])EM Smooth Lowess
(x, y[, theta, frac, it, int_method])Lowess Smooth smooth
(df, group_columns, target_columns[, …])DataFrame Smooth Method include lowess and emsmooth Methods Documentation
-
static
EMSmooth
(x, y, theta=2, threshold=10, int_method='')¶ EM Smooth
Parameters: - x – list | np.array | pd.Series
- y – list | np.array | pd.Series
- theta – x times of error
- threshold – only higher than this can be thought as abnormal value
- int_method – int methods ‘’ | ‘ceil’ | ‘floor’ | ‘int’
Returns: np.array
-
static
Lowess
(x, y, theta=3, frac=0.3, it=2, int_method='')¶ Lowess Smooth
Parameters: - x – list | np.array | pd.Series
- y – list | np.array | pd.Series
- theta – x times of error
- frac – Between 0 and 1. The fraction of the data used when estimating each y-value.
- it – The number of residual-based reweightings to perform.
- int_method – int methods ‘’ | ‘ceil’ | ‘floor’ | ‘int’
Returns: np.array
-
static
smooth
(df, group_columns, target_columns, smooth_method='lowess', theta=-1.0, frac=-1.0, it=-1.0, threshold=-1.0, int_method='')¶ DataFrame Smooth Method include lowess and emsmooth
Parameters: - df – DataFrame
- group_columns – column may contain different values which should treat individually
- target_columns – column containing values needed to be smoothed
- smooth_method –
- theta – x times of error
- frac – Between 0 and 1. The fraction of the data used when estimating each y-value.
- it – The number of residual-based reweightings to perform.
- threshold – only higher than this can be thought as abnormal value
- int_method – int methods ‘’ | ‘ceil’ | ‘floor’ | ‘int’
Returns: DataFrame
-
static


Chapter 7 Annotation
When you get the peaks table or features table, annotation of the peaks would help you. Check this review(Domingo-Almenara et al. 2018) for a detailed notes on annotation. They proposed five levels regarding currently computational annotation strategies.
Level 1: Peak Grouping: MS Psedospectra extraction based on peak shape similarity and peak abundance correlation
Level 2: Peak Annotation: Adducts, Neutral losses, isotopes, and other mass relationships based on mass distances
Level 3: Biochemical knowledge based on putative identification, potential biochemical reaction and related statistical analysis
Level 4: Use and intergration of tandem MS data based on data dependant/independent acquistion mode or in silico predction
Level 5: Retention time prediction based on library-available retention index or quantitative structure-retnetion relationships (QSRR) models.
Most of the softwares are at level 1 or 2. If we only have compounds structure, we could guess ions under different ionization method. If we have mass spectrum, we could match the mass spectral by a similarity analysis to the database. In metabolomics, we only have mass spectrum or mass-to-charge ratios. Single mass-to-charge ratio is not enough for identification. That’s the one bottleneck for annotation. So prediction is always performed on MS/MS data.
7.1 Issues in annotation
The major issue in annotation is the redundancy peaks from same metabolite. Unlike genomcis, peaks or featuers from peak selection are not independant with each other. Adducts, in-source fragments and isotopes would lead to missannotation. A commen solution is that use known adducts, neutral losses, molecular multimers or multipley charged ions to compare mass distances.
Another issue is about the MS/MS database. Only 10% of known metabolites in databases have experimental spectral data. Thus in silico prediction are required. Some works try to fill the gap between experimental data, theoretical values(from chemical database like chemspider) and prediction together. Here is a nice review about MS/MS prediction(Hufsky, Scheubert, and Böcker 2014).
7.2 Peak misidentification
- Isomer
Use seperation methods such as chromatography, ion mobility MS, MS/MS. Reversed-phase ion-pairing chromatography and HILIC is useful.Chemical derivatization is another options.
- Interfering compounds
20ppm is the least resolution and accuracy for HRMS.
- In-source degradation products
7.3 Annotation v.s. identification
According to the defination from the Chemical Analysis Working Group of the Metabolomics Standards Intitvative(Sumner et al. 2007; Viant et al. 2017). Four levels of confidence could be assigned to identification:
- Level 1 ‘identified metabolites’
- Level 2 ‘Putatively annotated compounds’
- Level 3 ‘Putatively characterised compound classes’
- Level 4 ‘Unknown’
In practice, data analysis based annotation could reach level 2. For level 1, we need at extra methods such as MS/MS, retention time, accurate mass, 2D NMR spectra, and so on to confirm the compounds. However, standards are always required for solid proof.
7.4 Cheminformatics
- RDKit Open-Source Cheminformatics Software
- cdk The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
- Open Babel Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
7.5 MS Database for annotation
7.5.1 MS/MS
MoNA Platform to collect all other open source database
GNPS use inner correlationship in the data and make network analysis at peaks’ level instand of annotated compounds to annotate the data(Wang et al. 2016).
ReSpect: phytochemicals
Metlin is another useful online application for annotation(Guijas et al. 2018).
LipidBlast: in silico prediction
NIST: Not free
7.6 Compounds Database
PubChem is an open chemistry database at the National Institutes of Health (NIH).
Chemspider is a free chemical structure database providing fast text and structure search access to over 67 million structures from hundreds of data sources.
ChEBI is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
RefMet A Reference list of Metabolite names.
CAS Largest substance database
7.7 Software
7.7.1 Adducts list
You could find adducts list here from commonMZ project.
7.7.2 Molgen
molgen generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures.
7.7.3 Isotope
Isotope pattern prediction
7.7.4 mfFinder
mfFinder predict formula based on accurate mass
7.7.5 CAMERA
Common annotation for xcms workflow(Kuhl et al. 2012).
7.7.6 RAMClustR
The software could be found here(Broeckling et al. 2014). The package included a vignette as usages. Use the following code to read:
7.7.7 pmd
Paired Mass Distance(PMD) analysis for GC/LC-MS based nontarget analysis to find independant peaks(???)
7.7.8 nontarget
nontarget Isotope & adduct peak grouping, homologue series detection
7.7.11 MINE
MINE is an open access database of computationally predicted enzyme promiscuity products for untargeted metabolomics. The annotation would be accurate for general compounds database.
7.7.12 InterpretMSSpectrum
This package is for annotate and interpret deconvoluted mass spectra (mass*intensity pairs) from high resolution mass spectrometry devices. You could use this package to find molecular ions for GC-MS.
7.7.13 For Ident
For-ident could give a score for identification with the help of logD(relative retention time) and/or MS/MS.
7.7.14 Retip
Retip Retention Time Prediction for Compound Annotation in Untargeted Metabolomics (???)
7.7.15 Binner
Binner Deep annotation of untargeted LC-MS metabolomics data (???)
7.7.16 mzmatch
Use the following code to install this package:
7.7.17 mz.unity
You could find source code here(Mahieu et al. 2016) and it’s for detecting and exploring complex relationships in accurate-mass mass spectrometry data.
7.7.19 ProbMetab
Provides probability ranking to candidate compounds assigned to masses, with the prior assumption of connected sample and additional previous and spectral information modeled by the user. You could find source code here(Silva et al. 2014).
7.7.20 RAMSI
You could find paper here(Baran and Northen 2013).
7.7.21 Sirius
Sirius is a new java-based software framework(Dührkop et al. 2015) for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry. It could be used with CSI:FingerID.
7.7.23 Plantmat
excel library based pridiction for plant metabolites(Qiu et al. 2016).
7.7.26 MolFind
JAVA based MolFind could make annotation for unknown chemical structure by prediction based on RI, ECOM50, drift time and CID spectra(Menikarachchi et al. 2012).
7.7.27 MetFusion
Java based integration of compound identiﬁcation strategies. You could access the application here(Gerlich and Neumann 2013).
7.7.28 iMet
This online application is a network-based computation method for annotation(Aguilar-Mogas et al. 2017).
7.7.29 Metscape
Metscape based on Debiased Sparse Partial Correlation (DSPC) algorithm(Basu et al. 2017) to make annotation.
7.7.30 MetFrag
MetFrag could be used to make in silico prediction/match of MS/MS data(Ruttkies et al. 2016).
7.7.31 LipidFrag
LipidFrag could be used to make in silico prediction/match of lipid related MS/MS data(Witting et al. 2017).
7.7.32 MycompoundID
MycompoundID could be used to search known and unknown metabolites(Li et al. 2013) online.
7.7.33 magma
magma could predict and match MS/MS files.
7.7.34 MetExpert
MetExpert is an expert system to assist users with limited expertise in informatics to interpret GCMS data for metabolite identification without querying spectral databases(Qiu, Lei, and Sumner 2018)
7.7.35 MS-DIA
decoMS2 requires two different collision energies, low (usually 0V) and high, in each precursor range to solve the mathematical equations.(Nikolskiy et al. 2013)
MS-DIAL data independent MS/MS deconvolution for comprehensive metabolome analysis.(Tsugawa et al. 2015)
MetDIA Targeted Metabolite Extraction of Multiplexed MS/MS Spectra Generated by Data-Independent Acquisition(???)
DIA-Umpire comprehensive computational framework for data-independent acquisition proteomics(Tsou et al. 2015)
MetaboDIA quantitative metabolomics analysis using DIA-MS(Chen et al. 2017)
SWATHtoMRM Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery(Zha et al. 2018)
References
Aguilar-Mogas, Antoni, Marta Sales-Pardo, Miriam Navarro, Roger Guimerà, and Oscar Yanes. 2017. “iMet: A Network-Based Computational Tool to Assist in the Annotation of Metabolites from Tandem Mass Spectra.” Anal. Chem. 89 (6): 3474–82. https://doi.org/10.1021/acs.analchem.6b04512.
Allen, Felicity, Allison Pon, Michael Wilson, Russ Greiner, and David Wishart. 2014. “CFM-ID: A Web Server for Annotation, Spectrum Prediction and Metabolite Identification from Tandem Mass Spectra.” Nucleic Acids Res 42 (W1): W94–W99. https://doi.org/10.1093/nar/gku436.
Baran, Richard, and Trent R. Northen. 2013. “Robust Automated Mass Spectra Interpretation and Chemical Formula Calculation Using Mixed Integer Linear Programming.” Anal. Chem. 85 (20): 9777–84. https://doi.org/10.1021/ac402180c.
Basu, Sumanta, William Duren, Charles R. Evans, Charles F. Burant, George Michailidis, and Alla Karnovsky. 2017. “Sparse Network Modeling and Metscape-Based Visualization Methods for the Analysis of Large-Scale Metabolomics Data.” Bioinformatics 33 (10): 1545–53. https://doi.org/10.1093/bioinformatics/btx012.
Broeckling, C. D., F. A. Afsar, S. Neumann, A. Ben-Hur, and J. E. Prenni. 2014. “RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based Annotation for Metabolomics Data.” Anal. Chem. 86 (14): 6812–7. https://doi.org/10.1021/ac501530d.
Chen, Gengbo, Scott Walmsley, Gemmy C. M. Cheung, Liyan Chen, Ching-Yu Cheng, Roger W. Beuerman, Tien Yin Wong, Lei Zhou, and Hyungwon Choi. 2017. “Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.” Anal. Chem. 89 (9): 4897–4906. https://doi.org/10.1021/acs.analchem.6b05006.
Domingo-Almenara, Xavier, J. Rafael Montenegro-Burke, H. Paul Benton, and Gary Siuzdak. 2018. “Annotation: A Computational Solution for Streamlining Metabolomics Analysis.” Anal. Chem. 90 (1): 480–89. https://doi.org/10.1021/acs.analchem.7b03929.
Dührkop, Kai, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker. 2015. “Searching Molecular Structure Databases with Tandem Mass Spectra Using CSI:FingerID.” PNAS 112 (41): 12580–5. https://doi.org/10.1073/pnas.1509788112.
Fernández-Albert, Francesc, Rafael Llorach, Cristina Andrés-Lacueva, and Alexandre Perera. 2014. “An R Package to Analyse LC/MS Metabolomic Data: MAIT (Metabolite Automatic Identification Toolkit).” Bioinformatics 30 (13): 1937–9. https://doi.org/10.1093/bioinformatics/btu136.
Gerlich, Michael, and Steffen Neumann. 2013. “MetFusion: Integration of Compound Identification Strategies.” J. Mass Spectrom. 48 (3): 291–98. https://doi.org/10.1002/jms.3123.
Guijas, Carlos, J. Rafael Montenegro-Burke, Xavier Domingo-Almenara, Amelia Palermo, Benedikt Warth, Gerrit Hermann, Gunda Koellensperger, et al. 2018. “METLIN: A Technology Platform for Identifying Knowns and Unknowns.” Anal. Chem. 90 (5): 3156–64. https://doi.org/10.1021/acs.analchem.7b04424.
Hufsky, Franziska, Kerstin Scheubert, and Sebastian Böcker. 2014. “Computational Mass Spectrometry for Small-Molecule Fragmentation.” TrAC Trends in Analytical Chemistry 53 (January): 41–48. https://doi.org/10.1016/j.trac.2013.09.008.
Koelmel, Jeremy P., Nicholas M. Kroeger, Candice Z. Ulmer, John A. Bowden, Rainey E. Patterson, Jason A. Cochran, Christopher W. W. Beecher, Timothy J. Garrett, and Richard A. Yost. 2017. “LipidMatch: An Automated Workflow for Rule-Based Lipid Identification Using Untargeted High-Resolution Tandem Mass Spectrometry Data.” BMC Bioinformatics 18 (July): 331. https://doi.org/10.1186/s12859-017-1744-3.
Kuhl, Carsten, Ralf Tautenhahn, Christoph Böttcher, Tony R. Larson, and Steffen Neumann. 2012. “CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets.” Anal. Chem. 84 (1): 283–89. https://doi.org/10.1021/ac202450g.
Li, Liang, Ronghong Li, Jianjun Zhou, Azeret Zuniga, Avalyn E. Stanislaus, Yiman Wu, Tao Huan, et al. 2013. “MyCompoundID: Using an Evidence-Based Metabolome Library for Metabolite Identification.” Anal. Chem. 85 (6): 3401–8. https://doi.org/10.1021/ac400099b.
Mahieu, Nathaniel G., Jonathan L. Spalding, Susan J. Gelman, and Gary J. Patti. 2016. “Defining and Detecting Complex Peak Relationships in Mass Spectral Data: The Mz.Unity Algorithm.” Anal. Chem. 88 (18): 9037–46. https://doi.org/10.1021/acs.analchem.6b01702.
Menikarachchi, Lochana C., Shannon Cawley, Dennis W. Hill, L. Mark Hall, Lowell Hall, Steven Lai, Janine Wilder, and David F. Grant. 2012. “MolFind: A Software Package Enabling HPLC/MS-Based Identification of Unknown Chemical Structures.” Anal. Chem. 84 (21): 9388–94. https://doi.org/10.1021/ac302048x.
Nikolskiy, Igor, Nathaniel G. Mahieu, Ying-Jr Chen, Ralf Tautenhahn, and Gary J. Patti. 2013. “An Untargeted Metabolomic Workflow to Improve Structural Characterization of Metabolites.” Anal. Chem. 85 (16): 7713–9. https://doi.org/10.1021/ac400751j.
Qiu, Feng, Dennis D. Fine, Daniel J. Wherritt, Zhentian Lei, and Lloyd W. Sumner. 2016. “PlantMAT: A Metabolomics Tool for Predicting the Specialized Metabolic Potential of a System and for Large-Scale Metabolite Identifications.” Anal. Chem. 88 (23): 11373–83. https://doi.org/10.1021/acs.analchem.6b00906.
Qiu, Feng, Zhentian Lei, and Lloyd W. Sumner. 2018. “MetExpert: An Expert System to Enhance Gas Chromatography-Mass Spectrometry-Based Metabolite Identifications.” Analytica Chimica Acta, Analytical Metabolomics, 1037 (December): 316–26. https://doi.org/10.1016/j.aca.2018.03.052.
Ruttkies, Christoph, Emma L. Schymanski, Sebastian Wolf, Juliane Hollender, and Steffen Neumann. 2016. “MetFrag Relaunched: Incorporating Strategies Beyond in Silico Fragmentation.” Journal of Cheminformatics 8 (January): 3. https://doi.org/10.1186/s13321-016-0115-9.
Silva, Ricardo R., Fabien Jourdan, Diego M. Salvanha, Fabien Letisse, Emilien L. Jamin, Simone Guidetti-Gonzalez, Carlos A. Labate, and Ricardo Z. N. Vêncio. 2014. “ProbMetab: An R Package for Bayesian Probabilistic Annotation of LCMS-Based Metabolomics.” Bioinformatics 30 (9): 1336–7. https://doi.org/10.1093/bioinformatics/btu019.
Sumner, Lloyd W., Alexander Amberg, Dave Barrett, Michael H. Beale, Richard Beger, Clare A. Daykin, Teresa W.-M. Fan, et al. 2007. “Proposed Minimum Reporting Standards for Chemical Analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI).” Metabolomics 3 (3): 211–21. https://doi.org/10.1007/s11306-007-0082-2.
Treutler, Hendrik, Hiroshi Tsugawa, Andrea Porzel, Karin Gorzolka, Alain Tissier, Steffen Neumann, and Gerd Ulrich Balcke. 2016. “Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.” Anal. Chem. 88 (16): 8082–90. https://doi.org/10.1021/acs.analchem.6b01569.
Tsou, Chih-Chiang, Dmitry Avtonomov, Brett Larsen, Monika Tucholska, Hyungwon Choi, Anne-Claude Gingras, and Alexey I. Nesvizhskii. 2015. “DIA-Umpire: Comprehensive Computational Framework for Data-Independent Acquisition Proteomics.” Nat. Methods 12 (3): 258–64. https://doi.org/10.1038/nmeth.3255.
Tsugawa, Hiroshi, Tomas Cajka, Tobias Kind, Yan Ma, Brendan Higgins, Kazutaka Ikeda, Mitsuhiro Kanazawa, Jean VanderGheynst, Oliver Fiehn, and Masanori Arita. 2015. “MS-DIAL: Data-Independent MS/MS Deconvolution for Comprehensive Metabolome Analysis.” Nat Meth 12 (6): 523–26. https://doi.org/10.1038/nmeth.3393.
Uppal, Karan, Douglas I. Walker, and Dean P. Jones. 2017. “xMSannotator: An R Package for Network-Based Annotation of High-Resolution Metabolomics Data.” Anal. Chem. 89 (2): 1063–7. https://doi.org/10.1021/acs.analchem.6b01214.
Viant, Mark R, Irwin J Kurland, Martin R Jones, and Warwick B Dunn. 2017. “How Close Are We to Complete Annotation of Metabolomes?” Current Opinion in Chemical Biology, Omics, 36 (February): 64–69. https://doi.org/10.1016/j.cbpa.2017.01.001.
Wang, Mingxun, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen, et al. 2016. “Sharing and Community Curation of Mass Spectrometry Data with Global Natural Products Social Molecular Networking.” Nat. Biotechnol. 34 (8): 828–37. https://doi.org/10.1038/nbt.3597.
Weber, Ralf J. M., and Mark R. Viant. 2010. “MI-Pack: Increased Confidence of Metabolite Identification in Mass Spectra by Integrating Accurate Masses and Metabolic Pathways.” Chemometrics and Intelligent Laboratory Systems, OMICS, 104 (1): 75–82. https://doi.org/10.1016/j.chemolab.2010.04.010.
Witting, Michael, Christoph Ruttkies, Steffen Neumann, and Philippe Schmitt-Kopplin. 2017. “LipidFrag: Improving Reliability of in Silico Fragmentation of Lipids and Application to the Caenorhabditis Elegans Lipidome.” PLOS ONE 12 (3): e0172311. https://doi.org/10.1371/journal.pone.0172311.
Zha, Haihong, Yuping Cai, Yandong Yin, Zhuozhong Wang, Kang Li, and Zheng-Jiang Zhu. 2018. “SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery.” Anal. Chem. 90 (6): 4062–70. https://doi.org/10.1021/acs.analchem.7b05318.


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20 Dec 2013
The 1984 Roadmap
One of my favorite books is George Orwell’s 1984. As a reader that is drawn to darker dystopian and apocalyptic works, 1984 is equally fascinating and horrifying. And yet, given the confirmed level (Snowden) of monitoring we face by our government in the name of “Security” we are as a whole, remarkably indifferent.
“There was of course no way of knowing whether you were being watched at any given moment. How often, or on what system, the Thought Police plugged in on any individual wire was guesswork. It was even conceivable that they watched everybody all the time. But at any rate they could plug in your wire whenever they wanted to. You had to live—did live, from habit that became instinct—in the assumption that every sound you made was overheard, and, except in darkness, every movement scrutinized.”
This quote has become our reality. A reality not of the government’s making but our own. A gilded cage built on a desire for faster and more accessible lives. In 1984 the telescreen was a requirement for every party member. In our world, the government works through more overt yet equally intrusive channels.
Why then does the government’s intrusion not piss more people off for longer periods of time? For example, I have a good idea of some of the data sources that the government is leeching information about me off.  I don’t after all have to use Facebook, or Google+.
Ultimately the reason I don’t shut things down is the same reason that I think most people don’t – Convenience.
And in the end, at least in my own case, I’m pretty boring. If the government wants to collect my drivel, the occasional zing I make about a neighbor or politician isn’t really worth much in the grand scheme of things.
Til next time,
Stephen Lange


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Starship Entertainment makes announcement warning legal action
by jennywillStarship Entertainment will be taking legal action.
MONSTA X's current situation involving Wonho and Shownu has unfortunately brought an incredible amount of hate comments. There has also been a doctored photo of Shownu floating around.
Starship Entertainment has warned of legal action for both malicious comments and the distribution of Shownu's photo. You can read their full statement below:
Hopefully this will help stave off some of the hate comments.


Definitions
- Dokuportal
- Tutorial
- Dokuportal
- Linux
- Setup your Account
- Qt Creator
- C++
- node handle basiertes threading
- c++ threading
- shared pointer/pointer etc.
- TemplatePackage
- ROS Essentials -> Link zum ROS Tutorial -> Danach Verweis auf unser Template Repository
- parameter
- config
- load from parameter server
- dynamic reconfigure
- launch
- Publisher
- Subscriber
- Service Client
- Service Server
- Action Server
- Action Client
- msg, srv, actions generation
- gtests
- capabilities and applications
- ROS Packages
- TF: Listener and Subscriber
- URDF, SDF
- Move It
- Move Base
- Localization (amcl)
- etc.
- Doxygen
- Summary
- Unit Documentation (e.g. UR5, iGPS, SLAM etc.)
- IGM Specialist
- Source Code Link
- Doxygen Link
- External Links
- Technical Documentation: Logins, Components, Turn on, Turn off
- GitLab Repository
- arduino [optional]
- folder for arduino sketch files
- matlab [optional]
- folder for matlab m files
- ros
- action
- CustomExample.action
- cfg
- SimpleTemplateNode.cfg
- config
- publisher_node.yaml
- include
- template_package
- libsimple_example_class
- simple_template_node
- launch
- publisher_node.launch
- msg
- CustomExample.msg
- src
- libsimple_example_class
- simple_template_node
- simple_template.cpp
- tools simple_template_node.cpp
- srv
- CustomExample.srv
- test
- libsimple_example
- conduct_heavy_computation_test.cpp
- CMakeLists.txt
- package.xml
- .gitignore
- .gitlab-ci.yml
- automatic doxygen creation for development branch
- Generation of UML class diagrams
- doc
- Doxyfile
- Correct the include path of header files that it can be used directly in ROS (add the package name es prefix) (idea by Henrik)
- Add todo and bug list to the start
- Doxygen:
- The CI will automatically run for the development branch
- The following lists are created for our documentation
- ROS:
- Always use Package XML format 2
- Always use c++11
- Namespaces for securing wrong includation (Henrik) -> Result: ALWAYS use namespaces of package
- Include handling and folder structures -> package_name/include/package_name -> necessary and important for including headers of other packages -> "global" headers (inlclude) and "local" headers (src) -> put all libraries into include -> keep node header file in src
- Order of public, private and protected in header file -> public -> protected
-> private
- Cpp template classes in header or cpp (Sascha) Conclusion: -> Standard without template -> Header, Cpp -> Template Class -> Only header
- Normal Class with template functions -> header (with template functions) + Cpp
- Rules for Cpp splitting for node class
- Use only one cpp files and do everything in it (Small Nodes)
- For the simple_template_node we have the following cpp:
- Split into multiple cpps (Big Nodes)
- The following cpps are allowed in addition to the node cpp:
- dynamic_reconfigure.cpp
- publications.cpp
- services.cpp
- subscriptions.cpp
- actions.cpp
ToDo
- Dokuportal: Read access for all users that have the link for the repository (still need to ask for getting access to the repo) (Florian)
- Source Code linked in Doxygen automatically (Tobi)
- Example: Doxygen of Perfect ROS Repository -> Source Code of do_something_action_node
- Doxygen:
- header files with correct include paths -> add package path before header name (Tobi)
- Solved! Needs to be done for every repo itself
- Create complete class diagram (Tobi)
- Solved! Each class should have its complete class diagram now
- Simplification of doxygen possible? -> Tests for best practice (Tobi)
- How to make filter for msg/srv/action executable when cloning? (Henrik)
- summit_bringup
- global launch files Doxygen? -> Try to find solution (Tobi)
- Pending!
- Make template package compilable and runable (Henrik)
- Put Threads into same structure as defined during last meeting (Johanna)
- Find solution for action clients and action services within our template (Henrik)
- Package XML Package format 2 (Marius)
- ROSTESTS: still available or deprecated? -> Henrik
- Deprecated? --> nice for testing overall nodes, or for example publishing rate
- particularly selftest is promising
- at the end it's a launch file
- to be examined by ALL (particularly for integration purposes with multiple nodes)
- CMakeLists: If clause for tests -> Henrik
- Possible? --> For release build might save some time -> recommended by Henrik
- CMakeLists
- What is the correct way to link the self-written library? (Henrik)
- coar_libs repository
- put to ROS_PACKAGE for easier integration
Want to get rid of the whole cpp-classes inside of the executable definition (Sascha)
- for now, sufficient to write cpp-classes seperately
- might change in future
- simple way to implement, but requires cmake to run when new file is added (is this even a problem?)
~~~ file(GLOB_RECURSE do_something_big_sources "src/do_something_big/*.cpp") add_executable(${PROJECT_NAME}_do_something_big_node src/do_something_big_node.cpp ${do_something_big_sources} ) ~~~
Next Discussion Points:
- Metapackages as a container for all the releated packages of e.g a robot (Henrik)
- default metapackages for robots? mobile robots and manipulators?
- Naming of packages that are related to a special unit: Name of robot always as prefix (Tobi)
- summit_description -> URDF
- summit_navigation -> MoveBase
- summit_teleoperation -> PS3 Controller
- summit_bringup -> global launch files
- ...
- Henrik: if necessary, useful (summit already done in this way)
Shall we make a rule for our repo that we do not use ros
as a folder anymore? We can just create a meta-package on the first level with a good name -> The difference between real
ROS repos and our ones is very very close with this strategy!
- only add other folders like
matlab
and arduino
if they exist -> they are not an issue when they exist within a ROS workspace
- This would mean that we also can define a metapackage for the whole repository (CMakeLists.txt and package.xml files on first level)
--> we keep the ros folder (majority's wish)
- Used Version of C++
- We need to define a C++ version for our whole development group -> Otherwise we will have many different compiler versions and perhaps some features (in higher C++ versions) that are not considered in older versions
- Options: C++ 98, C++ 03, C++ 11, C++ 14, C++ 17
- Open questions:
- Who is using which version?
Is it clever to always go for the latest?
C++ 11 definitely -> Standard C++14? (auto, lambda(?) expressions are useful features) C++17? (ISO certified at the end of 2017 -> wait?)
1. Is it enough to use this compile option within the CMakeLists.txt file or is there more to have in mind:
~~~
add_compile_options(-std=c++11)
~~~
* c++14 works with gcc6
* keep in mind warnings for ROS compapility
* QtCreator 5.9 requires gcc4.9
- To reduce compile time, we should move #include tags from the .h files to the respective .cpp files (if possible)
- Extend the gitlab tutorial section with the correct use of master, development, feature_xyz branchs?
- definitely (Henrik: Tobi)
Reopen discussion about template classes (Henrik und Sascha)
- There are other habbits in the online community? (Henrik)
- No, but: Aufteilen in zwei Files wäre möglich, beispielsweise durch eine .tpp datei
~~~ // x.h file
template <typename T> class X { void add(T a, T b); };
#include "x.tpp"
// x.tpp file
tempate <typename T>
void X<T>::add(T a, Tb) {}
~~~
* which file ending to chose: hpp (->pcl) oder tpp
* to discuss: problem: h should be hpp --> TBD
* .tpp seems to be common
- We need a small example for understanding the basics of shared pointer! Who is doing this? :) --> Sascha
- Outlook for the future (Tobi): All of our rules will be implemented in a Style Checking Test Suite that will run for every push onto the GitLab via CI. This means that all of our repos will converge towards this example repository slowly but surely!
- Shall we integrate clang formatting to our repos? (Tobi)
- Shall we get rid of the following doxygen commands as they are automatically created by GitLab
- Author
- Version
- Date
-> Only - Author
- in the future
Shall define standard prefixes for the main ros data types?
- Publisher: pub_*name*
- Subscriber: sub_*name*
- Service Client: client_*name*
- Service Server: server_*name*
- Action Client: aclient_*name*
- Action Server: aserver_*name*
- Messages: msg_*name*
- Services: srv_*name*
- Actions: action_*name*
- Transformations: tf_*name*
-> Contributing Guide and documentation in Tutorial but not strict rule
- Shall we use the "lib" prefix also for our folders within the /src folder? Or shall we only put it in front of the .so files? -> When you use "add_library" within the CMakeLists the prefix "lib" is created automatically
- Is someone capable of creating a shell script or even GUI to ease the process of creating a package from the template (Automatically parsing placeholders, ...)
- Merge all the folders into our big meta package [Henrik]
- Fill content for description package [Tobi]
- Member and global variables Idea Henrik:
- Member: m_variable (ROS: variable_)
- Global: g_variable
m_pub_example_publisher = nh.advertise...
m_energie = m_masse * m_gravitation * m_hoehe energie_ = masse_ * graviation_ * hoehe_ energie = masse * graviation * hoehe
energie = masse_ * gravitation * hoehe_ energie = m_masse * graviation * m_hoehe
-> UNDERSCORE
- Ask Johanna if her version is done within the solution of Henrik of if anything is missing about threading?
Notes during Meeting
- Alternative "Meeting" on Thursday, 14
- All Summits for testing --> More AP for WiFi
- Tobi and Marius prepare the novel Kinect Mounting until Monday
We do not need "initialize" and "shutdown" anymore -> The "run" method is enough for every node -> everything else is done within the constructor or deconstructor -> When we always use smart pointer we do not need to change the default deconstructor
-> Perhaps we need some information about data management and memory management (Henrik, Sascha) -> Going to be a new Repository as it is not ROS related -> New year: Move discussion about perfect ROS repository to SKILL SHARING discussion -> Qt Debugger -> Cpp Data Management -> Modern c++ features: Smart pointers Move semantics Lambdas Templates Initializer lists -> Data oriented design (dod) Dod in general Overgeneralization Last minute decision making Efficient data structures
-> Compilers Compiler options (gcc, clang, …) Compiler flags
-> Tools Compiler explorer Perf Google benchmark library
- Next level for development -> We can create bash scripts for creating template-based new elements as nodes -> GUI possible (Marius)
Best Practices
- When you use a service and you do not know how long it takes for computation -> put it into a thread (Johanna)
- Always use single package for custom message generation! -> Integrate it in the corresponding metapackage
Explanations for documentation
- Package.xml -> Necessary for rosdep install etc. for finding dependent packages


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main
- Static variable in class com.tabuto.jsimlife.views.
Launcher
main(String[])
- Static method in class com.tabuto.jsimlife.views.
Launcher
JSimLife Entry Point
mainView
- Variable in class com.tabuto.jsimlife.actions.
AddCellAction
mainView
- Variable in class com.tabuto.jsimlife.actions.
AddSeedAction
mainView
- Variable in class com.tabuto.jsimlife.actions.
LaunchXMLEasyEditorAction
mainView
- Variable in class com.tabuto.jsimlife.actions.
LoadSimulationAction
mainView
- Variable in class com.tabuto.jsimlife.actions.
SaveAsSimulationAction
mainView
- Variable in class com.tabuto.jsimlife.actions.
SaveSimulationAction
mainView
- Variable in class com.tabuto.jsimlife.actions.
ShowAboutInfoAction
mainView
- Variable in class com.tabuto.jsimlife.actions.
ShowChartViewAction
mainView
- Variable in class com.tabuto.jsimlife.views.
JSLMenu
makeMyDna()
- Method in class com.tabuto.jsimlife.
Zetatron
Add to this ZLifeDNA the Current Genes.
makeNavigationButton(String, AbstractAction, String, String)
- Method in class com.tabuto.jsimlife.views.
JSLToolbar
Add a JButton to this Toolbar
markColor
- Variable in class com.tabuto.jsimlife.actions.
MarkZlifeAction
marked
- Variable in class com.tabuto.jsimlife.
Zlife
marked()
- Method in class com.tabuto.jsimlife.
Zlife
Mark this ZLife with a green boundary rectangle.
marked(Color)
- Method in class com.tabuto.jsimlife.
Zlife
Mark this ZLife woth a 'c' Colored rectangle
markedButton
- Variable in class com.tabuto.jsimlife.views.
JSLSelectedZlifeView
markedColor
- Variable in class com.tabuto.jsimlife.
Zlife
markedColorButton
- Variable in class com.tabuto.jsimlife.views.
JSLSelectedZlifeView
MarkZlifeAction
- Class in
com.tabuto.jsimlife.actions
Class extends AbstractAction to perform the following Action: Mark the selected Zlife
MarkZlifeAction(JSimLife, Color)
- Constructor for class com.tabuto.jsimlife.actions.
MarkZlifeAction
Instantiate new MarkZlifeAction
MarkZlifeAction(JSimLife)
- Constructor for class com.tabuto.jsimlife.actions.
MarkZlifeAction
Instantiate new MarkZlifeAction
MarkZlifeAction(JSimLife, JButton)
- Constructor for class com.tabuto.jsimlife.actions.
MarkZlifeAction
Instantiate new MarkZlifeAction taking color from a JButton
MAX_CELL_NUMBER
- Variable in class com.tabuto.jsimlife.
JSimLife
Max ZLifes number
MAX_DENSITY
- Variable in class com.tabuto.jsimlife.
Seed
Max density values
MAX_RADIUS
- Variable in class com.tabuto.jsimlife.
Seed
Max radius value
MAX_SEEDS
- Variable in class com.tabuto.jsimlife.
Configuration
Seeds max number
MAX_SEEDS
- Variable in class com.tabuto.jsimlife.
JSimLife
Max number of seed element game can show
MAX_ZETATRON
- Variable in class com.tabuto.jsimlife.
Configuration
Zetatron max number
MAX_ZETATRON_NUMBER
- Variable in class com.tabuto.jsimlife.
JSimLife
Max Zetatron number
MAX_ZLIFES
- Variable in class com.tabuto.jsimlife.
Configuration
Zlifes max number
MAX_ZRETADOR
- Variable in class com.tabuto.jsimlife.
Configuration
Zretador max number
MAX_ZRETADOR_NUMBER
- Variable in class com.tabuto.jsimlife.
JSimLife
Max Zredator number
maxEnergy
- Variable in class com.tabuto.jsimlife.
JSLStatistic
maxEnergy
- Variable in class com.tabuto.jsimlife.
Zlife
maxEnergySlider
- Variable in class com.tabuto.jsimlife.views.
JSLNewCellView
MaxSeedsField
- Variable in class com.tabuto.jsimlife.views.
JSLPreferencesView
MaxSeedsLabel
- Variable in class com.tabuto.jsimlife.views.
JSLPreferencesView
MaxZetatronField
- Variable in class com.tabuto.jsimlife.views.
JSLPreferencesView
MaxZetatronLabel
- Variable in class com.tabuto.jsimlife.views.
JSLPreferencesView
MaxZlifesField
- Variable in class com.tabuto.jsimlife.views.
JSLPreferencesView
MaxZlifesLabel
- Variable in class com.tabuto.jsimlife.views.
JSLPreferencesView
MaxZretadorsField
- Variable in class com.tabuto.jsimlife.views.
JSLPreferencesView
MaxZretadorsLabel
- Variable in class com.tabuto.jsimlife.views.
JSLPreferencesView
menu
- Variable in class com.tabuto.jsimlife.views.
JSLMainView
merge(Dna)
- Method in class com.tabuto.jenetic.
Dna
This method merge this Dna with other and return a new Dna Code.
merge(Dna, Dna)
- Static method in class com.tabuto.jenetic.
Dna
Static
method returns a new Dna as a parametric merge between two same-size Dna.
mergeable
- Variable in class com.tabuto.jenetic.
Gene
Flag to determinate if this Gene supported Genetic Recombination.
metabolism
- Variable in class com.tabuto.jsimlife.
Zlife
metabolismSlider
- Variable in class com.tabuto.jsimlife.views.
JSLNewCellView
minEnergy
- Variable in class com.tabuto.jsimlife.
JSLStatistic
MinimumSize
- Variable in class com.tabuto.j2dgf.gui.
J2DBottomPanel
Minimum Panel Size
MinimumSize
- Variable in class com.tabuto.j2dgf.gui.
J2DControlPanel
Minimum Panel Size
module
- Variable in class com.tabuto.util.
Vettore
Vettore's module
mouseClicked(MouseEvent)
- Method in class com.tabuto.jsimlife.views.
JSLSimulationView
mouseEntered(MouseEvent)
- Method in class com.tabuto.jsimlife.views.
JSLSimulationView
mouseExited(MouseEvent)
- Method in class com.tabuto.jsimlife.views.
JSLSimulationView
mousePressed(MouseEvent)
- Method in class com.tabuto.jsimlife.views.
JSLSimulationView
mouseReleased(MouseEvent)
- Method in class com.tabuto.jsimlife.views.
JSLSimulationView
move()
- Method in interface com.tabuto.j2dgf.
Drawable
Override this method to implements the routines to move your object
move()
- Method in class com.tabuto.j2dgf.
Group
Moves all the Sprite
move()
- Method in class com.tabuto.j2dgf.
Sprite
Calculate the new Sprite position coordinate in terms of speed and angle and actual position
move()
- Method in class com.tabuto.jsimlife.
Zlife
move()
- Method in class com.tabuto.jsimlife.
Zretador
moveTo(double, double)
- Method in class com.tabuto.j2dgf.
Sprite
Set sprite's angle direction in order to reach the nx,ny coordinate's point
moveTo(Point)
- Method in class com.tabuto.j2dgf.
Sprite
Set sprite's direction in order to reach the Point p
moveTo(Sprite)
- Method in class com.tabuto.j2dgf.
Sprite
Set sprite's direction in order to reach the Sprite s
multiplierSlider
- Variable in class com.tabuto.jsimlife.views.
JSLNewCellView
myMlPerceptron
- Variable in class com.tabuto.jsimlife.
ZetatronBrain
MultiLayer Perceptron net provides by Neuroph package
MyUtils
- Class in
com.tabuto.util
Class
MyUtils
provides Static facilities multi-purphose methods.
MyUtils()
- Constructor for class com.tabuto.util.
MyUtils
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public class PrimaryIndex<PK,E>
extends java.lang.Object
PrimaryIndex
objects are thread-safe. Multiple threads may
safely call the methods of a shared PrimaryIndex
object.
PrimaryIndex
implements EntityIndex
to map the primary
key type (PK) to the entity type (E).
The Entity
annotation may be used to define an entity class and
the PrimaryKey
annotation may be used to define a primary key as
shown in the following example.
@Entity class Employee { @PrimaryKey long id; String name; Employee(long id, String name) { this.id = id; this.name = name; } private Employee() {} // For bindings }
To obtain the PrimaryIndex
for a given entity class, call EntityStore.getPrimaryIndex
, passing the
primary key class and the entity class. For example:
EntityStore store = new EntityStore(...);
PrimaryIndex<Long, Employee>
primaryIndex =
store.getPrimaryIndex(Long.class, Employee.class);
Note that Long.class
is passed as the primary key class, but the
primary key field has the primitive type long
. When a primitive
primary key field is used, the corresponding primitive wrapper class is used
to access the primary index. For more information on key field types, see
PrimaryKey
.
The PrimaryIndex
provides the primary storage and access methods
for the instances of a particular entity class. Entities are inserted and
updated in the PrimaryIndex
by calling a method in the family of
put(E)
methods. The put(E)
method will insert the entity if no
entity with the same primary key already exists. If an entity with the same
primary key does exist, it will update the entity and return the existing
(old) entity. For example:
Employee oldEntity; oldEntity = primaryIndex.put(new Employee(1, "Jane Smith")); // Inserts an entity assert oldEntity == null; oldEntity = primaryIndex.put(new Employee(2, "Joan Smith")); // Inserts an entity assert oldEntity == null; oldEntity = primaryIndex.put(new Employee(2, "Joan M. Smith")); // Updates an entity assert oldEntity != null;
The putNoReturn(E)
method can be used to avoid the overhead of
returning the existing entity, when the existing entity is not important to
the application. The return type of putNoReturn(E)
is void. For
example:
primaryIndex.putNoReturn(new Employee(1, "Jane Smith")); // Inserts an entity primaryIndex.putNoReturn(new Employee(2, "Joan Smith")); // Inserts an entity primaryIndex.putNoReturn(new Employee(2, "Joan M. Smith")); // Updates an entity
The putNoOverwrite(E)
method can be used to ensure that an existing
entity is not overwritten. putNoOverwrite(E)
returns true if the
entity was inserted, or false if an existing entity exists and no action was
taken. For example:
boolean inserted; inserted = primaryIndex.putNoOverwrite(new Employee(1, "Jane Smith")); // Inserts an entity assert inserted; inserted = primaryIndex.putNoOverwrite(new Employee(2, "Joan Smith")); // Inserts an entity assert inserted; inserted = primaryIndex.putNoOverwrite(new Employee(2, "Joan M. Smith")); // No action was taken! assert !inserted;
Primary key values must be unique, in other words, each instance of a
given entity class must have a distinct primary key value. Rather than
assigning the unique primary key values yourself, a sequence can be
used to assign sequential integer values automatically, starting with the
value 1 (one). A sequence is defined using the PrimaryKey.sequence()
annotation property. For example:
@Entity class Employee { @PrimaryKey(sequence="ID") long id; String name; Employee(String name) { this.name = name; } private Employee() {} // For bindings }
The name of the sequence used above is "ID". Any name can be used. If
the same sequence name is used in more than one entity class, the sequence
will be shared by those classes, in other words, a single sequence of
integers will be used for all instances of those classes. See PrimaryKey.sequence()
for more information.
Any method in the family of put(E)
methods may be used to insert
entities where the primary key is assigned from a sequence. When the put(E)
method returns, the primary key field of the entity object will be set
to the assigned key value. For example:
Employee employee; employee = new Employee("Jane Smith"); primaryIndex.putNoReturn(employee); // Inserts an entity assert employee.id == 1; employee = new Employee("Joan Smith"); primaryIndex.putNoReturn(employee); // Inserts an entity assert employee.id == 2;
This begs the question: How do you update an existing entity, without
assigning a new primary key? The answer is that the put(E)
methods
will only assign a new key from the sequence if the primary key field is
zero or null (for reference types). If an entity with a non-zero and
non-null key field is passed to a put(E)
method, any existing entity
with that primary key value will be updated. For example:
Employee employee; employee = new Employee("Jane Smith"); primaryIndex.putNoReturn(employee); // Inserts an entity assert employee.id == 1; employee = new Employee("Joan Smith"); primaryIndex.putNoReturn(employee); // Inserts an entity assert employee.id == 2; employee.name = "Joan M. Smith"; primaryIndex.putNoReturn(employee); // Updates an existing entity assert employee.id == 2;
Since PrimaryIndex
implements the EntityIndex
interface,
it shares the common index methods for retrieving and deleting entities,
opening cursors and using transactions. See EntityIndex
for more
information on these topics.
Note that when using an index, keys and values are stored and retrieved by value not by reference. In other words, if an entity object is stored and then retrieved, or retrieved twice, each object will be a separate instance. For example, in the code below the assertion will always fail.
MyKey key = ...; MyEntity entity1 = new MyEntity(key, ...); index.put(entity1); MyEntity entity2 = index.get(key); assert entity1 == entity2; // always fails!
| Constructor and Description |
|---|
PrimaryIndex(Database database,
java.lang.Class<PK> keyClass,
EntryBinding<PK> keyBinding,
java.lang.Class<E> entityClass,
EntityBinding<E> entityBinding)
Creates a primary index without using an
EntityStore . |
| Modifier and Type | Method and Description |
|---|---|
boolean |
contains(K key)
Checks for existence of a key in this index.
|
boolean |
contains(Transaction txn,
K key,
LockMode lockMode)
Checks for existence of a key in this index.
|
long |
count()
Returns a non-transactional count of the entities in this index.
|
boolean |
delete(K key)
Deletes all entities with a given index key.
|
boolean |
delete(Transaction txn,
K key)
Deletes all entities with a given index key.
|
EntityCursor<E> |
entities()
Opens a cursor for traversing all entities in this index.
|
EntityCursor<E> |
entities(K fromKey,
boolean fromInclusive,
K toKey,
boolean toInclusive)
Opens a cursor for traversing entities in a key range.
|
EntityCursor<E> |
entities(Transaction txn,
CursorConfig config)
Opens a cursor for traversing all entities in this index.
|
EntityCursor<E> |
entities(Transaction txn,
K fromKey,
boolean fromInclusive,
K toKey,
boolean toInclusive,
CursorConfig config)
Opens a cursor for traversing entities in a key range.
|
E |
get(PK key)
Gets an entity via a key of this index.
|
E |
get(Transaction txn,
PK key,
LockMode lockMode)
Gets an entity via a key of this index.
|
Database |
getDatabase()
Returns the underlying database for this index.
|
EntityBinding<E> |
getEntityBinding()
Returns the entity binding for this index.
|
java.lang.Class<E> |
getEntityClass()
Returns the entity class for this index.
|
EntryBinding<PK> |
getKeyBinding()
Returns the primary key binding for this index.
|
java.lang.Class<PK> |
getKeyClass()
Returns the primary key class for this index.
|
EntityCursor<K> |
keys()
Opens a cursor for traversing all keys in this index.
|
EntityCursor<K> |
keys(K fromKey,
boolean fromInclusive,
K toKey,
boolean toInclusive)
Opens a cursor for traversing keys in a key range.
|
EntityCursor<K> |
keys(Transaction txn,
CursorConfig config)
Opens a cursor for traversing all keys in this index.
|
EntityCursor<K> |
keys(Transaction txn,
K fromKey,
boolean fromInclusive,
K toKey,
boolean toInclusive,
CursorConfig config)
Opens a cursor for traversing keys in a key range.
|
java.util.Map<PK,E> |
map()
Returns a standard Java map based on this entity index.
|
E |
put(E entity)
Inserts an entity and returns null, or updates it if the primary key
already exists and returns the existing entity.
|
E |
put(Transaction txn,
E entity)
Inserts an entity and returns null, or updates it if the primary key
already exists and returns the existing entity.
|
boolean |
putNoOverwrite(E entity)
Inserts an entity and returns true, or returns false if the primary key
already exists.
|
boolean |
putNoOverwrite(Transaction txn,
E entity)
Inserts an entity and returns true, or returns false if the primary key
already exists.
|
void |
putNoReturn(E entity)
Inserts an entity, or updates it if the primary key already exists (does
not return the existing entity).
|
void |
putNoReturn(Transaction txn,
E entity)
Inserts an entity, or updates it if the primary key already exists (does
not return the existing entity).
|
java.util.SortedMap<PK,E> |
sortedMap()
Returns a standard Java sorted map based on this entity index.
|
public PrimaryIndex(Database database, java.lang.Class<PK> keyClass, EntryBinding<PK> keyBinding, java.lang.Class<E> entityClass, EntityBinding<E> entityBinding) throws DatabaseException
EntityStore
.
This constructor is not normally needed and is provided for
applications that wish to use custom bindings along with the Direct
Persistence Layer. Normally, getPrimaryIndex
is used instead.
Note that when this constructor is used directly, primary keys cannot
be automatically assigned from a sequence. The key assignment feature
requires knowledge of the primary key field, which is only available if
an EntityStore
is used. Of course, primary keys may be
assigned from a sequence manually before calling the put
methods in this class.
database
- the primary database.keyClass
- the class of the primary key.keyBinding
- the binding to be used for primary keys.entityClass
- the class of the entities stored in this index.entityBinding
- the binding to be used for entities.DatabaseException
- the base class for all BDB exceptions.public java.lang.Class<PK> getKeyClass()
public EntryBinding<PK> getKeyBinding()
public java.lang.Class<E> getEntityClass()
public EntityBinding<E> getEntityBinding()
public E put(E entity) throws DatabaseException
If a PrimaryKey.sequence()
is used and the primary key field of
the given entity is null or zero, this method will assign the next value
from the sequence to the primary key field of the given entity.
Auto-commit is used implicitly if the store is transactional.
entity
- the entity to be inserted or updated.DatabaseException
- the base class for all BDB exceptions.public E put(Transaction txn, E entity) throws DatabaseException
If a PrimaryKey.sequence()
is used and the primary key field of
the given entity is null or zero, this method will assign the next value
from the sequence to the primary key field of the given entity.
txn
- the transaction used to protect this operation, null to use
auto-commit, or null if the store is non-transactional.entity
- the entity to be inserted or updated.DatabaseException
- the base class for all BDB exceptions.public void putNoReturn(E entity) throws DatabaseException
put(Object)
to save the overhead of returning the existing
entity.
If a PrimaryKey.sequence()
is used and the primary key field of
the given entity is null or zero, this method will assign the next value
from the sequence to the primary key field of the given entity.
Auto-commit is used implicitly if the store is transactional.
entity
- the entity to be inserted or updated.DatabaseException
- the base class for all BDB exceptions.public void putNoReturn(Transaction txn, E entity) throws DatabaseException
put(Transaction,Object)
to save the overhead of returning the
existing entity.
If a PrimaryKey.sequence()
is used and the primary key field of
the given entity is null or zero, this method will assign the next value
from the sequence to the primary key field of the given entity.
txn
- the transaction used to protect this operation, null to use
auto-commit, or null if the store is non-transactional.entity
- the entity to be inserted or updated.DatabaseException
- the base class for all BDB exceptions.public boolean putNoOverwrite(E entity) throws DatabaseException
If a PrimaryKey.sequence()
is used and the primary key field of
the given entity is null or zero, this method will assign the next value
from the sequence to the primary key field of the given entity.
Auto-commit is used implicitly if the store is transactional.
entity
- the entity to be inserted.DatabaseException
- the base class for all BDB exceptions.public boolean putNoOverwrite(Transaction txn, E entity) throws DatabaseException
If a PrimaryKey.sequence()
is used and the primary key field of
the given entity is null or zero, this method will assign the next value
from the sequence to the primary key field of the given entity.
txn
- the transaction used to protect this operation, null to use
auto-commit, or null if the store is non-transactional.entity
- the entity to be inserted.DatabaseException
- the base class for all BDB exceptions.public E get(PK key) throws DatabaseException
EntityIndex
The operation will not be transaction protected, and LockMode.DEFAULT
is used implicitly.
key
- the key to search for.DatabaseException
- the base class for all BDB exceptions.public E get(Transaction txn, PK key, LockMode lockMode) throws DatabaseException
EntityIndex
txn
- the transaction used to protect this operation, or null
if the operation should not be transaction protected.key
- the key to search for.lockMode
- the lock mode to use for this operation, or null to
use LockMode.DEFAULT
.DatabaseException
- the base class for all BDB exceptions.public java.util.Map<PK,E> map()
EntityIndex
StoredMap
returned is defined by the Collections API. Stored collections conform
to the standard Java collections framework interface.public java.util.SortedMap<PK,E> sortedMap()
EntityIndex
StoredSortedMap
returned is defined by the Collections API. Stored collections conform
to the standard Java collections framework interface.public Database getDatabase()
EntityIndex
getDatabase
in interface EntityIndex<K,E>
public boolean contains(K key) throws DatabaseException
EntityIndex
The operation will not be transaction protected, and LockMode.DEFAULT
is used implicitly.
contains
in interface EntityIndex<K,E>
key
- the key to search for.DatabaseException
- the base class for all BDB exceptions.public boolean contains(Transaction txn, K key, LockMode lockMode) throws DatabaseException
EntityIndex
contains
in interface EntityIndex<K,E>
txn
- the transaction used to protect this operation, or null
if the operation should not be transaction protected.key
- the key to search for.lockMode
- the lock mode to use for this operation, or null to
use LockMode.DEFAULT
.DatabaseException
- the base class for all BDB exceptions.public long count() throws DatabaseException
EntityIndex
count
in interface EntityIndex<K,E>
DatabaseException
- the base class for all BDB exceptions.public boolean delete(K key) throws DatabaseException
EntityIndex
Auto-commit is used implicitly if the store is transactional.
delete
in interface EntityIndex<K,E>
key
- the key to search for.DatabaseException
- the base class for all BDB exceptions.public boolean delete(Transaction txn, K key) throws DatabaseException
EntityIndex
delete
in interface EntityIndex<K,E>
txn
- the transaction used to protect this operation, null to use
auto-commit, or null if the store is non-transactional.key
- the key to search for.DatabaseException
- the base class for all BDB exceptions.public EntityCursor<K> keys() throws DatabaseException
EntityIndex
The operations performed with the cursor will not be transaction
protected, and CursorConfig.DEFAULT
is used implicitly. If the
store is transactional, the cursor may not be used to update or delete
entities.
keys
in interface EntityIndex<K,E>
DatabaseException
- the base class for all BDB exceptions.public EntityCursor<K> keys(Transaction txn, CursorConfig config) throws DatabaseException
EntityIndex
keys
in interface EntityIndex<K,E>
txn
- the transaction used to protect all operations performed with
the cursor, or null if the operations should not be transaction
protected. If the store is non-transactional, null must be specified.
For a transactional store the transaction is optional for read-only
access and required for read-write access.config
- the cursor configuration that determines the default lock
mode used for all cursor operations, or null to implicitly use CursorConfig.DEFAULT
.DatabaseException
- the base class for all BDB exceptions.public EntityCursor<E> entities() throws DatabaseException
EntityIndex
The operations performed with the cursor will not be transaction
protected, and CursorConfig.DEFAULT
is used implicitly. If the
store is transactional, the cursor may not be used to update or delete
entities.
entities
in interface EntityIndex<K,E>
DatabaseException
- the base class for all BDB exceptions.public EntityCursor<E> entities(Transaction txn, CursorConfig config) throws DatabaseException
EntityIndex
entities
in interface EntityIndex<K,E>
txn
- the transaction used to protect all operations performed with
the cursor, or null if the operations should not be transaction
protected. If the store is non-transactional, null must be specified.
For a transactional store the transaction is optional for read-only
access and required for read-write access.config
- the cursor configuration that determines the default lock
mode used for all cursor operations, or null to implicitly use CursorConfig.DEFAULT
.DatabaseException
- the base class for all BDB exceptions.public EntityCursor<K> keys(K fromKey, boolean fromInclusive, K toKey, boolean toInclusive) throws DatabaseException
EntityIndex
The operations performed with the cursor will not be transaction
protected, and CursorConfig.DEFAULT
is used implicitly. If the
store is transactional, the cursor may not be used to update or delete
entities.
keys
in interface EntityIndex<K,E>
fromKey
- is the lower bound of the key range, or null if the range
has no lower bound.fromInclusive
- is true if keys greater than or equal to fromKey
should be included in the key range, or false if only keys greater than
fromKey should be included.toKey
- is the upper bound of the key range, or null if the range
has no upper bound.toInclusive
- is true if keys less than or equal to toKey should be
included in the key range, or false if only keys less than toKey should
be included.DatabaseException
- the base class for all BDB exceptions.public EntityCursor<K> keys(Transaction txn, K fromKey, boolean fromInclusive, K toKey, boolean toInclusive, CursorConfig config) throws DatabaseException
EntityIndex
keys
in interface EntityIndex<K,E>
txn
- the transaction used to protect all operations performed with
the cursor, or null if the operations should not be transaction
protected. If the store is non-transactional, null must be specified.
For a transactional store the transaction is optional for read-only
access and required for read-write access.fromKey
- is the lower bound of the key range, or null if the range
has no lower bound.fromInclusive
- is true if keys greater than or equal to fromKey
should be included in the key range, or false if only keys greater than
fromKey should be included.toKey
- is the upper bound of the key range, or null if the range
has no upper bound.toInclusive
- is true if keys less than or equal to toKey should be
included in the key range, or false if only keys less than toKey should
be included.config
- the cursor configuration that determines the default lock
mode used for all cursor operations, or null to implicitly use CursorConfig.DEFAULT
.DatabaseException
- the base class for all BDB exceptions.public EntityCursor<E> entities(K fromKey, boolean fromInclusive, K toKey, boolean toInclusive) throws DatabaseException
EntityIndex
The operations performed with the cursor will not be transaction
protected, and CursorConfig.DEFAULT
is used implicitly. If the
store is transactional, the cursor may not be used to update or delete
entities.
entities
in interface EntityIndex<K,E>
fromKey
- is the lower bound of the key range, or null if the range
has no lower bound.fromInclusive
- is true if keys greater than or equal to fromKey
should be included in the key range, or false if only keys greater than
fromKey should be included.toKey
- is the upper bound of the key range, or null if the range
has no upper bound.toInclusive
- is true if keys less than or equal to toKey should be
included in the key range, or false if only keys less than toKey should
be included.DatabaseException
- the base class for all BDB exceptions.public EntityCursor<E> entities(Transaction txn, K fromKey, boolean fromInclusive, K toKey, boolean toInclusive, CursorConfig config) throws DatabaseException
EntityIndex
entities
in interface EntityIndex<K,E>
txn
- the transaction used to protect all operations performed with
the cursor, or null if the operations should not be transaction
protected. If the store is non-transactional, null must be specified.
For a transactional store the transaction is optional for read-only
access and required for read-write access.fromKey
- is the lower bound of the key range, or null if the range
has no lower bound.fromInclusive
- is true if keys greater than or equal to fromKey
should be included in the key range, or false if only keys greater than
fromKey should be included.toKey
- is the upper bound of the key range, or null if the range
has no upper bound.toInclusive
- is true if keys less than or equal to toKey should be
included in the key range, or false if only keys less than toKey should
be included.config
- the cursor configuration that determines the default lock
mode used for all cursor operations, or null to implicitly use CursorConfig.DEFAULT
.DatabaseException
- the base class for all BDB exceptions.Copyright (c) 1996, 2016 Oracle and/or its affiliates. All rights reserved.


PatatapClone is a web application created using the javascript vector graphics scripting framework called paper.js
To see it in action you can press any key in your keyboard from a to z and the spacebar.
Tip: Turn up the volume!
PatatapClone is based on the Patatap application. Patatap can be found at https://patatap.com/
Jayme Bandeira, 2018


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Community Mart is an app-based local eCommerce. Order groceries, goods and supplies from our eStore partners. Download the app from Google Play and App Store today!
Drive Groceries allows for online, non-contact, same-day delivery, grocery shopping at the comfort of your own home.
GrocerGenie PH is an online grocery marketplace that enables users to purchase necessities and track orders.
Jungle allows online grocery shopping while offering a "Grocery Now, Pay Later" payment scheme.
MAD Market delivers fresh produce and baked goods directly from local farmers and SMEs.
Pushkart.ph is an on-demand online grocery delivery service that provides convenience and on-time delivery to its patrons.
Zagana delivers fresh produce straight from local farmers to support them during the pandemic.
Creator: DOH Philippines
Creator: Doc Willie Ong
Creator: Kurzgesagt – In a Nutshell


Game of Life
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Symmetric Polynomials
V3.1
A C++ library for generating symmetric polynomials with relations
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Let \(R=\mathbf Z[x_1,...,x_n]\); there is an obvious action on \(R\) by the symmetric group \(\Sigma_n\) and the fixed points \(R^{\Sigma_n}\) i.e. the symmetric polynomials, form a polynomial algebra on the elementary symmetric polynomials:
\[R^{\Sigma_n}=\mathbf Z[\sigma_1,...,\sigma_n]\]
where
\[\sigma_k(x_1,...,x_n)=\sum_{1\le i_1< \cdots< i_k\le n}x_{i_1}....x_{i_k}\]
Furthermore, there is a simple algorithm for writing every symmetric polynomial on the \(x_i\) as a polynomial on the \(\sigma_i\). This library implements that algorithm.
Let \(R=\mathbf Z[x_1,...,x_n,y_1,...,y_n]/(y_i^2=y_i)\); there is an obvious action on \(R\) by the symmetric group \(\Sigma_n\) permuting the \(x_i\) and \(y_i\) variables separately. A minimal description of the \(R^{\Sigma_n}\) is now more difficult:
\[R^{\Sigma_n}=\frac{\mathbf Z[\gamma_{s,i}]}{\gamma_{s,i}\gamma_{t,j}=r_{n,s,i,t,j}\gamma_{t,0}\gamma_{s,\min(i+j,n)}+\cdots}\]
where the "twisted Chern classes" are:
\[\gamma_{s,i}= \sum_{1\le j_1< \cdots< j_s\le n, 1\le k_1< \cdots< k_i\le n\\ j_u\neq k_v} x_{j_1}....x_{j_s}y_{k_1}\cdots y_{k_i}\]
for \(0\le s\le n\) and \(0\le i\le n-s\). The coefficient \(r_{n,s,i,t,j}\) in the relations is given by the binomial:
\[{\min(i+j+s,n)-t}\choose {j}\]
Moreover, the relations require the indices \(s,i,t,j\) to satisfy \(s\le t\le s+i\) and \(i,j>0\).
For convenience we set:
\[\alpha_i=\gamma_{0,i}=\sigma_i(y_1,...,y_n)\]
\[c_s=\gamma_{s,0}=\sigma_s(x_1,...,x_n)\]
Over \(\mathbf Q\), the \(\alpha_1^i\) can generate all \(\alpha_i\) via:
\[\alpha_i=\frac{\alpha(\alpha-1)\cdots(\alpha-i+1)}{i!}\]
however for speed+numerical stability we prefer to use all \(\alpha_i\) and have \(\mathbf Z\) coefficients in our relations.
This library implements an algorithm that can write every element in \(R^{\Sigma_n}\) as a polynomial on the generators \(\alpha_i,c_i,\gamma_{s,i}\) and further produce every relation explicitly.
The "twisted Pontryagin/symplectic classes" are defined as:
\[\kappa_{s,i}=\sum_{1\le j_1< \cdots< j_s\le n, 1\le k_1< \cdots< k_i\le n\\ j_u\neq k_v}x^2_{j_1}....x^2_{j_s}y_{k_1}\cdots y_{k_i}\]
This library also allows one to write the \(\kappa_{s,i}\) in terms of the \(\gamma_{s,i}\)


Recently Raspberry Pi Foundation released new version of thier product: Raspberry Pi 3. It has 64-bit quad-core ARM CPU and integerated wireless LAN. It is great thing to play with and I got it for myself.
Installation
Together with Raspberry Pi I have bought the standard case, power adapter and micro SD card with “NOOBS”. Assembling is trivial, you just put Raspberry Pi inside the case, insert micro SD card and plug HDMI cable into it. Do not forget about keyboard and mouse (I am not sure if you can follow installation process without mouse). Once powered the Raspberry Pi boots and installation starts. Depending on SD card you can choose operating system to install. In my case it was single one: Rasbian which is Debian based OS. Next, next, next and wait for a few minutes. Done.
Wireless mouse issues
During installation I have already noticed that my wireless mouse did not work properly. It was terribly lagging. I could still move it and click, but even clicking a few Next buttons was not trivial. My hope was that after installation it would get better. But no, the issue was still present. I briefly tried to find way to fix it but nothing worked. And since the plan was to connect to Raspberry pi via ssh I decided not to spend a few nights figuring out what was wrong with wireless mouse.
WIFI issues
Once installed you probably want to connect it to the Internet. Raspberry Pi 3 comes with integrated WIFI card. I connected it to my WIFI router and started Internet surfing (with terrible mouse experience). It worked a little bit until the WIFI connection dropped out. Interesting. The distance to router was quite small, around 4 meters without any obstacles. When the connection came back I have checked pings and it was terrible. The WIFI connection kept dropping every few minutes. After googling a little bit I have found people claiming that it might be related to power management. Let’s check if it helps:
sudo iwconfig wlan0 power off
During the next 10 minutes connection never dropped out and pings looked much better.
Ok, now let’s make it permanent, otherwise the power management would be back after the next reboot.
It can be disabled in /etc/network/interfaces
by adding post-up iwconfig wlan0 power off || true
for all wireless interfaces:
allow-hotplug wlan0
iface wlan0 inet manual
post-up iwconfig wlan0 power off || true
wpa-conf /etc/wpa_supplicant/wpa_supplicant.conf
allow-hotplug wlan1
iface wlan1 inet manual
post-up iwconfig wlan1 power off || true
wpa-conf /etc/wpa_supplicant/wpa_supplicant.conf
Autossh service
The next step is to setup autossh service. I want to connect to Raspberry pi via ssh from outside my local network.
The easiest choice for me is reverse ssh tunnel. ssh daemon is already present in Raspbian.
Installation of autossh is trivial: sudo apt-get install autossh
.
And the last step is to make sure that autossh starts reverse tunnel on system boot.
And here I realize upstart is missing from Raspbian. I was very surprised by that fact. Does it still use plain sysv?
Ok, should not be a problem: sudo apt-get install upstart. It gives some warnings, ignore them. Upstart is ready.
Then I created upstart service /etc/init/autossh.conf
to start autossh on boot. Verifying that it works:
sudo service autossh start
ps aux | grep ssh
Great, but on the next reboot autossh did not start. It was not even mentioned anywhere in /var/log/syslog
.
I took around 2 hours before I realized that Raspbian uses systemd. systemd, really? That was fast.
Not all people are in favor of switching to systemd. It’s maintly due to attidue of systemd developers. As example you can read their responses in this email discussions about kernel failure due to systemd. Go through these emails and also check links to the bugtracker with responses from systemd developers. They show very nice attitude when discussing kernel failure to boot on systems without cgroups (caused by systemd):
Lennart Poettering: To make this work we’d need a patch, as nobody of us tests this.
Ok, back to autossh issue. Can I remove systemd and use upstart. It looks like it would be very difficult to do.
So let’s make systemd service for autossh. Add new file /etc/systemd/system/autossh.service
:
[Unit]
Description=autossh tunnel
After=network-target nss-lookup.target
[Service]
Environment="AUTOSSH_GATETIME=0" # avoids stopping after first ssh failure
ExecStart=/usr/bin/autossh -M 0 -N -R 70000:<IP_ADDRESS>:22 -o "ServerAliveInterval 60" -o "ServerAliveCountMax 3" -o "StrictHostKeyChecking=no" -o "BatchMode=yes" -i private_key pi@remotecomputer
[Install]
WantedBy=multi-user.target
Enough of systemd scripts for today.


Have you ever dreamed of waking up each morning to fresh eggs laid by your very own chickens? That dream could easily be a reality - even if you live in a city! Raising backyard chickens has become a popular and rewarding alternative to store-bought eggs. Your days of debating cage free vs. free range are over!
One of our chickens, Eleanor


Generate 'SPSS'/'SAS' styled frequency tables. Frequency tables are generated with variable and value label attributes where applicable with optional html output to quickly examine datasets.
| Version: | 0.3.1 |
| Depends: | R (≥ 3.0), rmarkdown, knitr, DT, ggplot2 |
| Imports: | gtools, utils |
| Suggests: | foreign, haven, testthat, covr, shiny |
| Published: | 2018-10-28 |
| Author: | Alistair Wilcox |
| Maintainer: | Alistair Wilcox <frequency at alistairwilcox.com> |
| BugReports: | https://github.com/wilcoxa/frequency/issues |
| License: | GPL-3 |
| URL: | https://github.com/wilcoxa/frequency |
| NeedsCompilation: | no |
| SystemRequirements: | pandoc (>= 1.12.3) - http://pandoc.org |
| Materials: | README NEWS |
| CRAN checks: | frequency results |
| Reference manual: | frequency.pdf |
| Package source: | frequency_0.3.1.tar.gz |
| Windows binaries: | r-devel: frequency_0.3.1.zip, r-release: frequency_0.3.1.zip, r-oldrel: frequency_0.3.1.zip |
| OS X binaries: | r-release: frequency_0.3.1.tgz, r-oldrel: frequency_0.3.1.tgz |
Please use the canonical form https://CRAN.R-project.org/package=frequency to link to this page.


Welcome to guggmeta
Guggenheim Helsinki Design Competition
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